Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-01 12:07 -0400 (Wed, 01 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4843 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4631 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4575 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1920/2337 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Sconify 1.29.0 (landing page) Tyler J Burns
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the Sconify package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Sconify.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: Sconify |
Version: 1.29.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Sconify_1.29.0.tar.gz |
StartedAt: 2025-09-30 12:53:50 -0000 (Tue, 30 Sep 2025) |
EndedAt: 2025-09-30 12:57:33 -0000 (Tue, 30 Sep 2025) |
EllapsedTime: 223.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: Sconify.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Sconify_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Sconify.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Sconify/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Sconify’ version ‘1.29.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Sconify’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed SconeValues 18.266 0.129 32.562 ImputeTesting 5.367 0.023 9.983 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Iteration 900: error is 1.150102 (50 iterations in 0.25 seconds) Iteration 950: error is 1.148705 (50 iterations in 0.25 seconds) Iteration 1000: error is 1.146434 (50 iterations in 0.24 seconds) Fitting performed in 5.14 seconds. [ FAIL 2 | WARN 4 | SKIP 0 | PASS 70 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test.post.processing.R:53:5'): Testing the output of the tSNE vis function ── TsneVis(...) has type 'object', not 'list'. ── Failure ('test.post.processing.R:60:5'): Testing the output of the make.hist function ── MakeHist(wand.final, 100, "IL7.fraction.cond.2", "fraction IL7") has type 'object', not 'list'. [ FAIL 2 | WARN 4 | SKIP 0 | PASS 70 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.22-bioc/meat/Sconify.Rcheck/00check.log’ for details.
Sconify.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL Sconify ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘Sconify’ ... ** this is package ‘Sconify’ version ‘1.29.0’ ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to '/' Note: wrong number of arguments to 'asinh' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Sconify)
Sconify.Rcheck/tests/testthat.Rout.fail
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(Sconify) > > test_check("Sconify") Read the 100 x 27 data matrix successfully! OpenMP is working. 1 threads. Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000 Computing input similarities... Building tree... Done in 0.01 seconds (sparsity = 0.966000)! Learning embedding... Iteration 50: error is 50.785386 (50 iterations in 0.01 seconds) Iteration 100: error is 50.144954 (50 iterations in 0.01 seconds) Iteration 150: error is 49.412263 (50 iterations in 0.01 seconds) Iteration 200: error is 51.095186 (50 iterations in 0.02 seconds) Iteration 250: error is 50.786481 (50 iterations in 0.02 seconds) Iteration 300: error is 1.475726 (50 iterations in 0.01 seconds) Iteration 350: error is 0.924898 (50 iterations in 0.01 seconds) Iteration 400: error is 0.415903 (50 iterations in 0.01 seconds) Iteration 450: error is 0.193667 (50 iterations in 0.01 seconds) Iteration 500: error is 0.190356 (50 iterations in 0.01 seconds) Iteration 550: error is 0.188203 (50 iterations in 0.01 seconds) Iteration 600: error is 0.188664 (50 iterations in 0.01 seconds) Iteration 650: error is 0.188483 (50 iterations in 0.01 seconds) Iteration 700: error is 0.188238 (50 iterations in 0.01 seconds) Iteration 750: error is 0.189260 (50 iterations in 0.01 seconds) Iteration 800: error is 0.189006 (50 iterations in 0.01 seconds) Iteration 850: error is 0.189125 (50 iterations in 0.01 seconds) Iteration 900: error is 0.189068 (50 iterations in 0.01 seconds) Iteration 950: error is 0.188739 (50 iterations in 0.01 seconds) Iteration 1000: error is 0.188371 (50 iterations in 0.01 seconds) Fitting performed in 0.24 seconds. Read the 1000 x 27 data matrix successfully! OpenMP is working. 1 threads. Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000 Computing input similarities... Building tree... Done in 0.15 seconds (sparsity = 0.129120)! Learning embedding... Iteration 50: error is 64.878057 (50 iterations in 0.36 seconds) Iteration 100: error is 60.823401 (50 iterations in 0.26 seconds) Iteration 150: error is 60.321608 (50 iterations in 0.26 seconds) Iteration 200: error is 60.165077 (50 iterations in 0.28 seconds) Iteration 250: error is 60.113896 (50 iterations in 0.30 seconds) Iteration 300: error is 1.335000 (50 iterations in 0.24 seconds) Iteration 350: error is 1.230641 (50 iterations in 0.25 seconds) Iteration 400: error is 1.198620 (50 iterations in 0.25 seconds) Iteration 450: error is 1.185500 (50 iterations in 0.25 seconds) Iteration 500: error is 1.178682 (50 iterations in 0.23 seconds) Iteration 550: error is 1.173728 (50 iterations in 0.23 seconds) Iteration 600: error is 1.170526 (50 iterations in 0.23 seconds) Iteration 650: error is 1.166323 (50 iterations in 0.24 seconds) Iteration 700: error is 1.162218 (50 iterations in 0.26 seconds) Iteration 750: error is 1.157717 (50 iterations in 0.24 seconds) Iteration 800: error is 1.156299 (50 iterations in 0.25 seconds) Iteration 850: error is 1.152749 (50 iterations in 0.25 seconds) Iteration 900: error is 1.150102 (50 iterations in 0.25 seconds) Iteration 950: error is 1.148705 (50 iterations in 0.25 seconds) Iteration 1000: error is 1.146434 (50 iterations in 0.24 seconds) Fitting performed in 5.14 seconds. [ FAIL 2 | WARN 4 | SKIP 0 | PASS 70 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test.post.processing.R:53:5'): Testing the output of the tSNE vis function ── TsneVis(...) has type 'object', not 'list'. ── Failure ('test.post.processing.R:60:5'): Testing the output of the make.hist function ── MakeHist(wand.final, 100, "IL7.fraction.cond.2", "fraction IL7") has type 'object', not 'list'. [ FAIL 2 | WARN 4 | SKIP 0 | PASS 70 ] Error: Test failures Execution halted
Sconify.Rcheck/Sconify-Ex.timings
name | user | system | elapsed | |
FcsToTibble | 0.165 | 0.008 | 0.199 | |
Fnn | 0.250 | 0.188 | 0.438 | |
GetKnnDe | 0.104 | 0.000 | 0.104 | |
GetMarkerNames | 0.034 | 0.000 | 0.034 | |
ImputeTesting | 5.367 | 0.023 | 9.983 | |
MakeHist | 0.746 | 0.032 | 1.560 | |
MakeKnnList | 0.509 | 0.020 | 1.062 | |
MeaningOfLife | 0 | 0 | 0 | |
ParseMarkers | 0.294 | 0.004 | 0.603 | |
PostProcessing | 0.108 | 0.004 | 0.224 | |
ProcessMultipleFiles | 0.138 | 0.013 | 0.305 | |
QuantNormalizeElements | 0.307 | 0.000 | 0.611 | |
SconeValues | 18.266 | 0.129 | 32.562 | |
SplitFile | 0.112 | 0.000 | 0.226 | |
StringToNumbers | 0.000 | 0.000 | 0.001 | |
SubsampleAndTsne | 2.963 | 0.024 | 4.819 | |
TsneVis | 0.447 | 0.019 | 0.935 | |